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Immunological role of platelets in Theiler’s virus-induced inflammatory demyelinating disease and myocarditis

GSE253385 Mus musculus (mouse) RNA-seq (gene expression) 66 samples Submitted 2024/03/20 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 66 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
66 samples: 12 conditions, mostly with about 5 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Exploring the Role of Platelets in Virus-Induced Inflammatory Demyelinating Disease and MyocarditisInternational journal of molecular sciences · 2024
Summary (written by the submitters)
Platelets have been immunologically associated with viral and immune-mediated diseases such as Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) and Experimental autoim-mune encephalomyelitis (EAE). However, the role of platelets in Theiler’s murine encephalo-myelitis virus (TMEV)-induced myocarditis and inflammatory demyelination disease (IDD) is still unknown.
Read the full summary ↓
We determine whether platelets were associated with TMEV infection and whether glycoprotein Ib alpha chain (GPIbα/CD42b) antibody injection could affect the pathogenicity of TMEV-induced myocarditis and TMEV-IDD. We conducted a mechanistic experiment by injecting TMEV-infected mice with the anti-GPIbα antibodies 0 and 5 days p.i. (“Early” group) or 18 and 22 days p.i. (“Late” group). Using in silico and in vivo approaches, we found platelets and platelet-related genes were associated with TMEV infection. Platelet depletion in Early and Late mice reduced fibrotic area in the heart, inflammatory demyelinating lesions with lower viral persistence in the CNS and altered antiviral antibody responses. Thus, platelets contribute to the pathogenesis of TMEV infection by promoting fibrosis and CNS inflammation. Platelet-depletion treatment might open new therapeutic approaches for TMEV-induced myocarditis and TMEV-IDD.
Published in
Exploring the Role of Platelets in Virus-Induced Inflammatory Demyelinating Disease and Myocarditis
Ahmad I, Omura S, Sato F et al. · International journal of molecular sciences 2024 · PMID 38542433 · doi:10.3390/ijms25063460
This dataset
Open GSE253385 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE253385_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1065441 and SRA study SRP484037. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38542433) ↗
Study design
12 conditions, mostly with about 5 replicates each
Platelets from control mice on day 35 ×7 Platelets from TMEV-infected mice on day 35 ×7 Platelets from TMEV-infected mice on day 4 ×6 Platelets from TMEV-infected mice on day 7 ×6 Platelets from control mice on day 4 ×5 Platelets from control mice on day 7 ×5 Spleen from control mice on day 4 ×5 Spleen from TMEV-infected mice on day 4 ×5 +4 more

Supports a case/control comparison: 34 samples read as cases, 32 as controls.

How we read this: 12 replicated groups read from 66 sample titles; they account for 66 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 26 more — browse all 66 samples with per-sample file links →

Datasets on a similar topic

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